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(v0.6.1.9053) prerelease fixes

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dr. M.S. (Matthijs) Berends
2019-06-02 19:23:19 +02:00
parent 8de0495008
commit bd73988f15
38 changed files with 337 additions and 327 deletions
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2
man/AMR.Rd
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@ -31,7 +31,7 @@ This package can be used for:
Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Glasner[1], Alex W. Friedrich[1], Bhanu N.M. Sinha[1] \cr
[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - \url{rug.nl} \url{umcg.nl} \cr
[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - \url{https://www.rug.nl} \url{https://www.umcg.nl} \cr
[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{certe.nl}
}

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man/catalogue_of_life.Rd
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@ -28,7 +28,7 @@ Included are:
The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
The syntax used to transform the original data to a cleansed R format, can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R}.
The syntax used to transform the original data to a cleansed R format, can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R}.
}
\section{Read more on our website!}{

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man/microorganisms.Rd
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@ -4,25 +4,7 @@
\name{microorganisms}
\alias{microorganisms}
\title{Data set with ~65,000 microorganisms}
\format{A \code{\link{data.frame}} with 67,903 observations and 16 variables:
\describe{
\item{\code{mo}}{ID of microorganism as used by this package}
\item{\code{col_id}}{Catalogue of Life ID}
\item{\code{fullname}}{Full name, like \code{"Echerichia coli"}}
\item{\code{kingdom}}{Taxonomic kingdom of the microorganism}
\item{\code{phylum}}{Taxonomic phylum of the microorganism}
\item{\code{class}}{Taxonomic class of the microorganism}
\item{\code{order}}{Taxonomic order of the microorganism}
\item{\code{family}}{Taxonomic family of the microorganism}
\item{\code{genus}}{Taxonomic genus of the microorganism}
\item{\code{species}}{Taxonomic species of the microorganism}
\item{\code{subspecies}}{Taxonomic subspecies of the microorganism}
\item{\code{rank}}{Taxonomic rank of the microorganism, like \code{"species"} or \code{"genus"}}
\item{\code{ref}}{Author(s) and year of concerning scientific publication}
\item{\code{species_id}}{ID of the species as used by the Catalogue of Life}
\item{\code{source}}{Either \code{"CoL"}, \code{"DSMZ"} (see source) or "manually added"}
\item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
}}
\format{An object of class \code{data.frame} with 67903 rows and 16 columns.}
\source{
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).

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man/microorganisms.codes.Rd
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@ -4,7 +4,7 @@
\name{microorganisms.codes}
\alias{microorganisms.codes}
\title{Translation table for microorganism codes}
\format{A \code{\link{data.frame}} with 5,171 observations and 2 variables:
\format{A \code{\link{data.frame}} with 4,969 observations and 2 variables:
\describe{
\item{\code{certe}}{Commonly used code of a microorganism}
\item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}